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 5FJB | pdb_00005fjb

Cyclophilin A Stabilize HIV-1 Capsid through a Novel Non- canonical Binding Site


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.00 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5FJB

This is version 1.2 of the entry. See complete history. 

Literature

Cyclophilin a Stabilizes the HIV-1 Capsid Through a Novel Non-Canonical Binding Site.

Liu, C., Perilla, J.R., Ning, J., Lu, M., Hou, G., Ramalho, R., Himes, B.A., Zhao, G., Bedwell, G.J., Byeon, I., Ahn, J., Gronenborn, A.M., Prevelige, P.E., Rousso, I., Aiken, C., Polenova, T., Schulten, K., Zhang, P.

(2016) Nat Commun 7: 10714

  • DOI: https://doi.org/10.1038/ncomms10714
  • Primary Citation Related Structures: 
    5FJB

  • PubMed Abstract: 

    The host cell factor cyclophilin A (CypA) interacts directly with the HIV-1 capsid and regulates viral infectivity. Although the crystal structure of CypA in complex with the N-terminal domain of the HIV-1 capsid protein (CA) has been known for nearly two decades, how CypA interacts with the viral capsid and modulates HIV-1 infectivity remains unclear. We determined the cryoEM structure of CypA in complex with the assembled HIV-1 capsid at 8-Å resolution. The structure exhibits a distinct CypA-binding pattern in which CypA selectively bridges the two CA hexamers along the direction of highest curvature. EM-guided all-atom molecular dynamics simulations and solid-state NMR further reveal that the CypA-binding pattern is achieved by single-CypA molecules simultaneously interacting with two CA subunits, in different hexamers, through a previously uncharacterized non-canonical interface. These results provide new insights into how CypA stabilizes the HIV-1 capsid and is recruited to facilitate HIV-1 infection.


  • Organizational Affiliation: 
    • Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA.

Macromolecule Content 

  • Total Structure Weight: 66.6 kDa 
  • Atom Count: 4,664 
  • Modeled Residue Count: 600 
  • Deposited Residue Count: 600 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GAG POLYPROTEIN
A, B
218Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for P04591 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04591 
Go to UniProtKB:  P04591
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04591
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A164Homo sapiensMutation(s): 0 
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62937 (Homo sapiens)
Explore P62937 
Go to UniProtKB:  P62937
PHAROS:  P62937
GTEx:  ENSG00000196262 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62937
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.00 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONIHRSR
RECONSTRUCTIONSPIDER

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2017-08-23
    Changes: Data collection
  • Version 1.2: 2024-10-23
    Changes: Data collection, Database references, Refinement description, Structure summary